4-25260610-TTATATATATATATATATATA-TTATATATA

Variant names:

• chr4-25260610-TTATATATATATA-T
• rs533544057
• NM_018323.4:c.978+40_978+51delTATATATATATA

Variant summary

Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BS1 BS2

The NM_018323.4(PI4K2B):​c.978+40_978+51delTATATATATATA variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0129 in 306,586 control chromosomes in the GnomAD database, including 52 homozygotes. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: 𝑓 0.016 (33 hom., cov: 12)
  • Exomes 𝑓: 0.011 (19 hom.)
• Consequence: PI4K2B NM_018323.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.68

Genes affected

PI4K2B (HGNC:18215): (phosphatidylinositol 4-kinase type 2 beta) This gene encodes a member of the type II PI4 kinase protein family. The encoded protein is primarily cytosolic and contributes to overall PI4-kinase activity along with other protein family members. This protein is involved in early T cell activation. [provided by RefSeq, Dec 2016]

ACMG classification

Verdict is Benign. Variant got -8 ACMG points.

• BS1: Variant frequency is greater than expected in population afr. gnomad4 allele frequency = 0.016 (2157/135092) while in subpopulation AFR AF= 0.0263 (954/36252). AF 95% confidence interval is 0.0249. There are 33 homozygotes in gnomad4. There are 1034 alleles in male gnomad4 subpopulation. Median coverage is 12. This position pass quality control queck.
• BS2: High Homozygotes in GnomAd4 at 33 AR gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
PI4K2B	NM_018323.4	c.978+40_978+51delTATATATATATA		intron_variant	Intron 6 of 9	ENST00000264864.8	NP_060793.2
PI4K2B	XM_005248174.3	c.963+40_963+51delTATATATATATA		intron_variant	Intron 6 of 9		XP_005248231.1
PI4K2B	XM_005248175.5	c.690+40_690+51delTATATATATATA		intron_variant	Intron 6 of 9		XP_005248232.1
PI4K2B	NR_144633.2	n.1124+40_1124+51delTATATATATATA		intron_variant	Intron 6 of 9

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
PI4K2B	ENST00000264864.8	c.978+20_978+31delTATATATATATA		intron_variant	Intron 6 of 9	1	NM_018323.4	ENSP00000264864.6
PI4K2B	ENST00000512921.4	c.690+20_690+31delTATATATATATA		intron_variant	Intron 6 of 9	2		ENSP00000423373.1

Frequencies

GnomAD3 genomes AF: 0.0159 AC: 2153 AN: 135080 Hom.: 32 Cov.: 12

Gnomad AFR AF: 0.0262

Gnomad AMI AF: 0.00926

Gnomad AMR AF: 0.0189

Gnomad ASJ AF: 0.0127

Gnomad EAS AF: 0.00263

Gnomad SAS AF: 0.0105

Gnomad FIN AF: 0.00864

Gnomad MID AF: 0.0315

Gnomad NFE AF: 0.0118

Gnomad OTH AF: 0.0169

GnomAD3 exomes AF: 0.00699 AC: 258 AN: 36926 Hom.: 0 AF XY: 0.00651 AC XY: 127 AN XY: 19504

Gnomad AFR exome AF: 0.0105

Gnomad AMR exome AF: 0.00861

Gnomad ASJ exome AF: 0.00423

Gnomad EAS exome AF: 0.000996

Gnomad SAS exome AF: 0.00329

Gnomad FIN exome AF: 0.00652

Gnomad NFE exome AF: 0.00780

Gnomad OTH exome AF: 0.0112

GnomAD4 exome AF: 0.0106 AC: 1813 AN: 171494 Hom.: 19 AF XY: 0.0104 AC XY: 988 AN XY: 95370

Gnomad4 AFR exome AF: 0.0192

Gnomad4 AMR exome AF: 0.00987

Gnomad4 ASJ exome AF: 0.00815

Gnomad4 EAS exome AF: 0.00224

Gnomad4 SAS exome AF: 0.00514

Gnomad4 FIN exome AF: 0.00875

Gnomad4 NFE exome AF: 0.0116

Gnomad4 OTH exome AF: 0.0138

GnomAD4 genome AF: 0.0160 AC: 2157 AN: 135092 Hom.: 33 Cov.: 12 AF XY: 0.0160 AC XY: 1034 AN XY: 64604

Gnomad4 AFR AF: 0.0263

Gnomad4 AMR AF: 0.0189

Gnomad4 ASJ AF: 0.0127

Gnomad4 EAS AF: 0.00264

Gnomad4 SAS AF: 0.0103

Gnomad4 FIN AF: 0.00864

Gnomad4 NFE AF: 0.0118

Gnomad4 OTH AF: 0.0162

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs533544057; hg19: chr4-25262232;